[2014-05-29 19:12:07] Beginning TopHat run (v2.0.8b)
-----------------------------------------------
[2014-05-29 19:12:07] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 19:12:07] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 19:12:07] Checking for Bowtie index files
[2014-05-29 19:12:07] Checking for reference FASTA file
[2014-05-29 19:12:07] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 19:12:09] Preparing reads
	 left reads: min. length=60, max. length=101, 24951986 kept reads (1790 discarded)
[2014-05-29 19:22:20] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 19:53:54] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 19:56:06] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 19:58:29] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 20:01:00] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 20:03:35] Searching for junctions via segment mapping
[2014-05-29 20:07:14] Retrieving sequences for splices
[2014-05-29 20:09:09] Indexing splices
[2014-05-29 20:09:38] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 20:11:25] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 20:13:22] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 20:15:20] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 20:17:15] Joining segment hits
[2014-05-29 20:20:47] Reporting output tracks
-----------------------------------------------
[2014-05-29 20:34:26] Run complete: 01:22:19 elapsed